It's said that a picture is worth a thousand words.
Assuming you have installed the plugin, highlight a couple of tracks that have show leading zero(s) and click Tools > Additional Tagging Tools > Advanced search and replace...

Now that the ASR window is open, start typing "remove" in the upper window. That will filter out all the presents that DO NOT show the word "remove." Scroll down the list until you see "Remove leading zeros..." and you'll see two presents. To be honest, I don't know what the difference is between them - I always use the second one. Click on it (BUT NOT ON THE CHECKBOX) and it becomes selected. At this point you may have to use the drop-down to add "Track#" to <Tag 1>. Now click on "Preview" and the tracks you selected will appear along with a column showing the track number as is, and a column showing the result of the proposed tag change...

At this point click "Apply" and the tags will be changed...

I want to stress that you should test this a few times on a very small number of tracks to make sure it's behaving as you expect. Once you're satisfied, go back to the present and check the box to the left of the one you want to you want to have automatically applied. You could also check the box next to "Ask confirmation before autoapplying..." but you will have to click 'OK' each time the plugin wants to make a change, which can become quite tedious for a large number of times.
I hope this helps. If you have questions about other uses of this plugin, you should post them in the plugin's thread:
https://getmusicbee.com/forum/index.php?topic=3833.0